Author: tlinnet
Date: Thu Sep 18 17:46:44 2014
New Revision: 25900
URL: http://svn.gna.org/viewcvs/relax?rev=25900&view=rev
Log:
Reordered functions in repeated analysis protocol.
Task #7826 (https://gna.org/task/index.php?7826): Write an python class for
the repeated analysis of dispersion data.
Modified:
trunk/auto_analyses/relax_disp_repeat_cpmg.py
Modified: trunk/auto_analyses/relax_disp_repeat_cpmg.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/auto_analyses/relax_disp_repeat_cpmg.py?rev=25900&r1=25899&r2=25900&view=diff
==============================================================================
--- trunk/auto_analyses/relax_disp_repeat_cpmg.py (original)
+++ trunk/auto_analyses/relax_disp_repeat_cpmg.py Thu Sep 18 17:46:44
2014
@@ -449,6 +449,9 @@
else:
self.interpreter.results.write(file=resfile, dir=path,
force=force)
+ # Show selected spins
+ self.interpreter.spin.display()
+
def select_spin(self, spin_id=None, methods=None, model=None,
model_from=None, analysis=None, analysis_from=None, list_glob_ini=None,
force=False):
"""Method to select spins for a pipe."""
@@ -493,10 +496,12 @@
else:
self.interpreter.results.write(file=resfile, dir=path,
force=force)
-
- def r20_from_min_r2eff(self, spin_id=None, methods=None, model=None,
model_from=None, analysis=None, analysis_from=None, list_glob_ini=None,
force=False):
- """Will set the grid R20 values from the minimum R2eff values
through the r20_from_min_r2eff user function.
- This will speed up the grid search with a factor
GRID_INC^(Nr_spec_freq). For a CPMG experiment with two fields and standard
GRID_INC=21, the speed-up is a factor 441."""
+ # Show selected spins
+ self.interpreter.spin.display()
+
+
+ def value_set(self, spin_id=None, val=None, param=None, methods=None,
model=None, model_from=None, analysis=None, analysis_from=None,
list_glob_ini=None, force=False):
+ """Use value.set on all pipes."""
# Set default
if model_from == None:
@@ -523,13 +528,13 @@
self.interpreter.pipe.switch(pipe_name)
# Print
- subtitle(file=sys.stdout, text="Set grid r20 for pipe='%s'"
% (pipe_name), prespace=3)
+ subtitle(file=sys.stdout, text="For param '%s' set value
'%3.2f' for pipe='%s'" % (param, val, pipe_name), prespace=3)
# Select the model.
self.interpreter.relax_disp.select_model(model)
- # Set r20 from min r2eff.
- self.interpreter.relax_disp.r20_from_min_r2eff(force=True)
+ # Set value
+ self.interpreter.value.set(val=val, param=param,
spin_id=spin_id)
# Save results, and store the current settings dic to pipe.
cdp.settings = self.settings
@@ -541,9 +546,13 @@
else:
self.interpreter.results.write(file=resfile, dir=path,
force=force)
-
- def value_set(self, spin_id=None, val=None, param=None, methods=None,
model=None, model_from=None, analysis=None, analysis_from=None,
list_glob_ini=None, force=False):
- """Use value.set on all pipes."""
+ # Print for pipe name
+ self.spin_display_params(pipe_name=pipe_name)
+
+
+ def r20_from_min_r2eff(self, spin_id=None, methods=None, model=None,
model_from=None, analysis=None, analysis_from=None, list_glob_ini=None,
force=False):
+ """Will set the grid R20 values from the minimum R2eff values
through the r20_from_min_r2eff user function.
+ This will speed up the grid search with a factor
GRID_INC^(Nr_spec_freq). For a CPMG experiment with two fields and standard
GRID_INC=21, the speed-up is a factor 441."""
# Set default
if model_from == None:
@@ -570,10 +579,13 @@
self.interpreter.pipe.switch(pipe_name)
# Print
- subtitle(file=sys.stdout, text="For param '%s' set value
'%3.2f' for pipe='%s'" % (param, val, pipe_name), prespace=3)
-
- # Set value
- self.interpreter.value.set(val=val, param=param,
spin_id=spin_id)
+ subtitle(file=sys.stdout, text="Set grid r20 for pipe='%s'"
% (pipe_name), prespace=3)
+
+ # Select the model.
+ self.interpreter.relax_disp.select_model(model)
+
+ # Set r20 from min r2eff.
+ self.interpreter.relax_disp.r20_from_min_r2eff(force=True)
# Save results, and store the current settings dic to pipe.
cdp.settings = self.settings
@@ -585,6 +597,9 @@
else:
self.interpreter.results.write(file=resfile, dir=path,
force=force)
+ # Print for pipe name
+ self.spin_display_params(pipe_name=pipe_name)
+
def minimise_grid_search(self, inc=11, verbosity=0, methods=None,
model=None, model_from=None, analysis=None, analysis_from=None,
list_glob_ini=None, force=False):
"""Use value.set on all pipes."""
@@ -605,6 +620,11 @@
# Check previous, and get the pipe name.
found, pipe_name, resfile, path =
self.check_previous_result(method=self.method, model=model,
analysis=analysis, glob_ini=glob_ini, bundle=self.method)
+ # Try from analysis
+ if not found:
+ # Check previous, and get the pipe name.
+ found, pipe_name, resfile, path =
self.check_previous_result(method=self.method, model=model,
analysis=analysis_from, glob_ini=glob_ini, bundle=self.method)
+
if not found:
# If previous pipe not found, then create it.
model_from_pipe_name =
self.name_pipe(method=self.method, model=model_from, analysis=analysis_from,
glob_ini=glob_ini)
@@ -648,6 +668,12 @@
# Save results, and store the current settings dic to pipe.
cdp.settings = self.settings
+
+ # Define new pipe names.
+ pipe_name = self.name_pipe(method=self.method, model=model,
analysis=analysis, glob_ini=glob_ini)
+ resfile = pipe_name.replace(" ", "_")
+ model_path = model.replace(" ", "_")
+ path = self.results_dir+sep+model_path
if found and not force:
file_path = get_file_path(file_name=resfile, dir=path)
@@ -656,9 +682,12 @@
else:
self.interpreter.results.write(file=resfile, dir=path,
force=force)
-
- def minimise_execute(self, verbosity=1, methods=None, model=None,
model_from=None, analysis=None, analysis_from=None, list_glob_ini=None,
force=False):
- """Use value.set on all pipes."""
+ # Print for pipe name
+ self.spin_display_params(pipe_name=pipe_name)
+
+
+ def cluster_spins(self, spin_id=None, methods=None, model=None,
model_from=None, analysis=None, analysis_from=None, list_glob_ini=None,
force=False):
+ """Method to select spins for a pipe."""
# Set default
if model_from == None:
@@ -680,6 +709,58 @@
# If previous pipe not found, then create it.
model_from_pipe_name =
self.name_pipe(method=self.method, model=model_from, analysis=analysis_from,
glob_ini=glob_ini)
+ # Copy pipe and switch.
+
self.interpreter.pipe.copy(pipe_from=model_from_pipe_name, pipe_to=pipe_name,
bundle_to=self.method)
+ self.interpreter.pipe.switch(pipe_name)
+
+ # Print
+ subtitle(file=sys.stdout, text="Cluster spins '%s' for
pipe='%s'" % (spin_id, pipe_name), prespace=3)
+
+ # Select spins.
+ self.interpreter.relax_disp.cluster(cluster_id='sel',
spin_id=spin_id)
+
+ # Save results, and store the current settings dic to pipe.
+ cdp.settings = self.settings
+
+ if found and not force:
+ file_path = get_file_path(file_name=resfile, dir=path)
+ text = "The file '%s' already exists. Set the force
flag to True to overwrite." % (file_path)
+ warn(RelaxWarning(text))
+ else:
+ self.interpreter.results.write(file=resfile, dir=path,
force=force)
+
+ # print clustered spins
+ print("Clustered spins are:", cdp.clustering)
+
+
+ def minimise_execute(self, verbosity=1, methods=None, model=None,
model_from=None, analysis=None, analysis_from=None, list_glob_ini=None,
force=False):
+ """Use value.set on all pipes."""
+
+ # Set default
+ if model_from == None:
+ model_from = model
+ if analysis_from == None:
+ analysis_from = analysis
+
+ # Loop over the methods.
+ for method in methods:
+ # Change the self key.
+ self.set_self(key='method', value=method)
+
+ # Loop over the glob ini:
+ for glob_ini in list_glob_ini:
+ # Check previous, and get the pipe name.
+ found, pipe_name, resfile, path =
self.check_previous_result(method=self.method, model=model,
analysis=analysis, glob_ini=glob_ini, bundle=self.method)
+
+ # Try from analysis
+ if not found:
+ # Check previous, and get the pipe name.
+ found, pipe_name, resfile, path =
self.check_previous_result(method=self.method, model=model,
analysis=analysis_from, glob_ini=glob_ini, bundle=self.method)
+
+ if not found:
+ # If previous pipe not found, then create it.
+ model_from_pipe_name =
self.name_pipe(method=self.method, model=model_from, analysis=analysis_from,
glob_ini=glob_ini)
+
# Check if pipe exists. If not, try grid pipe.
if not pipes.has_pipe(model_from_pipe_name):
model_from_pipe_name =
self.name_pipe(method=self.method, model=model_from, analysis='grid',
glob_ini=glob_ini)
@@ -696,6 +777,25 @@
# Do the minimisation.
self.interpreter.minimise.execute(min_algor=self.min_algor,
func_tol=self.opt_func_tol, max_iter=self.opt_max_iterations,
constraints=self.constraints, scaling=True, verbosity=verbosity)
+
+ # Save results, and store the current settings dic to pipe.
+ cdp.settings = self.settings
+
+ # Define new pipe names.
+ pipe_name = self.name_pipe(method=self.method, model=model,
analysis=analysis, glob_ini=glob_ini)
+ resfile = pipe_name.replace(" ", "_")
+ model_path = model.replace(" ", "_")
+ path = self.results_dir+sep+model_path
+
+ if found and not force:
+ file_path = get_file_path(file_name=resfile, dir=path)
+ text = "The file '%s' already exists. Set the force
flag to True to overwrite." % (file_path)
+ warn(RelaxWarning(text))
+ else:
+ self.interpreter.results.write(file=resfile, dir=path,
force=force)
+
+ # Print for pipe name
+ self.spin_display_params(pipe_name=pipe_name)
def name_pipe(self, method, model, analysis, glob_ini, clusterid=None):
@@ -771,9 +871,46 @@
"""Display parameters for model in pipe."""
- # Switch to the pipe.
- if pipes.cdp_name() != pipe_name:
- self.interpreter.pipe.switch(pipe_name)
+ # First check if the pipe already exists. Then switch to it.
+ if pipes.has_pipe(pipe_name):
+ # Switch to the pipe.
+ if pipes.cdp_name() != pipe_name:
+ print("Detected the presence of previous '%s' pipe -
switching to it." % pipe_name)
+ self.interpreter.pipe.switch(pipe_name)
+
+ else:
+ # The result file.
+ pipe_name_split = pipe_name.split("_-_")
+ method = pipe_name_split[0]
+ model = pipe_name_split[1]
+ analysis = pipe_name_split[2]
+ bundle = method
+
+ model_path = model.replace(" ", "_")
+ path = self.results_dir+sep+model_path
+ # The result file.
+ resfile = pipe_name.replace(" ", "_")
+
+ # Check that results do not already exist - i.e. a previous run
was interrupted.
+ path1 = get_file_path(file_name=resfile, dir=path)
+ path2 = path1 + '.bz2'
+ path3 = path1 + '.gz'
+
+ #print("Path to R2eff file is: %s"%path1)
+ if access(path1, F_OK) or access(path2, F_OK) or access(path2,
F_OK):
+ # Printout.
+ print("Detected the presence of results files for the '%s'
pipe - loading these instead of performing optimisation for a second time." %
pipe_name)
+
+ # Create a data new pipe and switch to it.
+ self.interpreter.pipe.create(pipe_name=pipe_name,
pipe_type=self.pipe_type, bundle=bundle)
+ self.interpreter.pipe.switch(pipe_name)
+
+ # Load the results.
+ self.interpreter.results.read(file=resfile, dir=path)
+
+ # Set found to True
+ found = True
+
# Start dic.
my_dic = {}
@@ -814,7 +951,10 @@
my_dic[spin_id][param] = {}
# Get the Value.
- param_val = deepcopy(getattr(cur_spin,
param)[param_key])
+ if len(getattr(cur_spin, param)) == 0:
+ param_val = None
+ else:
+ param_val = deepcopy(getattr(cur_spin,
param)[param_key])
my_dic[spin_id][param][param_key] = param_val
# Add information to data.
r25900 - /trunk/auto_analyses/relax_disp_repeat_cpmg.py